| enhanced class count | 215 |
|---|
| enhanced classes | ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Home.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Contact.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.valid.ValidField pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/valid/ValidField.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/DownloadResults.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.ReturnToPageMessage pageSpecification=false specificationLocation=context:/WEB-INF/ReturnToPageMessage.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.GeneNeighborhood pageSpecification=false specificationLocation=context:/WEB-INF/GeneNeighborhood.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/CoverageStatistics.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/argo/JWSSequenceRange.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.ForBean pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/For.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.components.When pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/contrib/components/When.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.StatsTableLegend pageSpecification=false specificationLocation=context:/WEB-INF/StatsTableLegend.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.web.component.ContextScript pageSpecification=false specificationLocation=context:/WEB-INF/ContextScript.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.ObjectTextArea pageSpecification=false specificationLocation=context:/WEB-INF/ObjectTextArea.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.Delegator pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/Delegator.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.FeatureLink pageSpecification=false specificationLocation=context:/WEB-INF/FeatureLink.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.BindingExternalLink pageSpecification=false specificationLocation=context:/WEB-INF/BindingExternalLink.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.html.Describe pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/html/Describe.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Dotplot.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.FeatureDisplayOptions pageSpecification=false specificationLocation=context:/WEB-INF/FeatureDisplayOptions.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.Swatch pageSpecification=false specificationLocation=context:/WEB-INF/Swatch.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/News.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.DateRangeSelector pageSpecification=false specificationLocation=context:/WEB-INF/DateRangeSelector.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.Breadcrumbs pageSpecification=false specificationLocation=context:/WEB-INF/Breadcrumbs.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.FeatureLinks pageSpecification=false specificationLocation=context:/WEB-INF/FeatureLinks.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/CompareStrains.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.SearchForm pageSpecification=false specificationLocation=context:/WEB-INF/SearchForm.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.components.Choose pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/contrib/components/Choose.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.ElseBean pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/Else.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/AnnotationIndex.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/SysBioResourceIndex.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/SysBioHome.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Circular.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.RadioGroup pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/RadioGroup.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.EditIcon pageSpecification=false specificationLocation=context:/WEB-INF/EditIcon.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.AnnotationEdits pageSpecification=false specificationLocation=context:/WEB-INF/AnnotationEdits.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.html.Image pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/html/Image.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Info.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.web.component.ContextStylesheet pageSpecification=false specificationLocation=context:/WEB-INF/ContextStylesheet.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.SearchParameterEditor pageSpecification=false specificationLocation=context:/WEB-INF/SearchParameterEditor.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.GeneLink pageSpecification=false specificationLocation=context:/WEB-INF/GeneLink.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/global/CalhounException.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.TermLink pageSpecification=false specificationLocation=context:/WEB-INF/TermLink.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.GeneDetailsRow pageSpecification=false specificationLocation=context:/WEB-INF/GeneDetailsRow.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/SingleGenomeIndex.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.link.ExternalLink pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/link/ExternalLink.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GenomeMap.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.CollapsibleTableSection pageSpecification=false specificationLocation=context:/WEB-INF/CollapsibleTableSection.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.AjaxCaller pageSpecification=false specificationLocation=context:/WEB-INF/AjaxCaller.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GenomesIndex.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.PolymorphicSiteDisplay pageSpecification=false specificationLocation=context:/WEB-INF/PolymorphicSiteDisplay.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.FeatureOverlapLinks pageSpecification=false specificationLocation=context:/WEB-INF/FeatureOverlapLinks.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.InsertWithLinks pageSpecification=false specificationLocation=context:/WEB-INF/InsertWithLinks.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Blast.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/FeatureRegionHelp.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.Insert pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/Insert.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/argo/JnlpFile.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.NewWindowIcon pageSpecification=false specificationLocation=context:/WEB-INF/NewWindowIcon.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.JsonCall pageSpecification=false specificationLocation=context:/WEB-INF/JsonCall.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.Form pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/Form.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.SaveIcon pageSpecification=false specificationLocation=context:/WEB-INF/SaveIcon.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/QueryCounts.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/OrthologSearch.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/FeatureSearchResults.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneFinding.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.PubLink pageSpecification=false specificationLocation=context:/WEB-INF/PubLink.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Sitemap.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.Navigation pageSpecification=false specificationLocation=context:/WEB-INF/Navigation.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Regions.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/CAHome.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/AlignmentViewer.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.table.components.TablePages pageSpecification=false specificationLocation=context:/WEB-INF/CalhounTablePages.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.ConditionalWrapper pageSpecification=false specificationLocation=context:/WEB-INF/ConditionalWrapper.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.Submit pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/Submit.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/OrthologHelp.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/global/Login.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.FeatureActionForm pageSpecification=false specificationLocation=context:/WEB-INF/FeatureActionForm.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.Upload pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/Upload.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/AssemblyStats.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.html.RequestDisplay pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/html/RequestDisplay.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.Hidden pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/Hidden.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneDetailsByBioSequence.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.Substitute pageSpecification=false specificationLocation=context:/WEB-INF/Substitute.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.EpitopeSearch pageSpecification=false specificationLocation=context:/WEB-INF/EpitopeSearch.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=classpath:/org/apache/tapestry/contrib/table/components/inserted/SimpleTableColumnPage.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneIndex.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.Radio pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/Radio.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneStatsSummary.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/PairwiseComparisons.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/FeatureMap.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.ReleaseAssetLink pageSpecification=false specificationLocation=context:/WEB-INF/ReleaseAssetLink.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.DownloadEntry pageSpecification=false specificationLocation=context:/WEB-INF/DownloadEntry.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.Border pageSpecification=false specificationLocation=context:/WEB-INF/Border.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.StatsMapTable pageSpecification=false specificationLocation=context:/WEB-INF/StatsMapTable.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.SequenceDisplay pageSpecification=false specificationLocation=context:/WEB-INF/SequenceDisplay.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/ontology/Term.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.FeatureDisplayOptionsWithHelp pageSpecification=false specificationLocation=context:/WEB-INF/FeatureDisplayOptionsWithHelp.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Assembly.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Links.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.Toolbar pageSpecification=false specificationLocation=context:/WEB-INF/Toolbar.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneEnrichment.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.web.component.InsertJson pageSpecification=false specificationLocation=context:/WEB-INF/InsertJson.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.IfBean pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/If.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.table.components.TableColumns pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/contrib/table/components/TableColumns.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/ReseqStrainInfo.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.link.DirectLink pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/link/DirectLink.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneNeighborhoodPage.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.FrameSelector pageSpecification=false specificationLocation=context:/WEB-INF/FrameSelector.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.components.When pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/contrib/components/Otherwise.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneFamilyTreeOld.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.Foreach pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/Foreach.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/FeatureRedirect.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/OperonSearchResults.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.NavMenu pageSpecification=false specificationLocation=context:/WEB-INF/NavMenu.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.SearchResultsTable pageSpecification=false specificationLocation=context:/WEB-INF/SearchResultsTable.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.CALink pageSpecification=false specificationLocation=context:/WEB-INF/CALink.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.TranscriptImage pageSpecification=false specificationLocation=context:/WEB-INF/TranscriptImage.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.table.components.inserted.SimpleTableColumnComponent pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/contrib/table/components/inserted/SimpleTableColumnComponent.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/CategorySearchResults.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/MutationSearch.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.DynamicDownloadLink pageSpecification=false specificationLocation=context:/WEB-INF/DynamicDownloadLink.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneLocus.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/maps/Index.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.Dashboard pageSpecification=false specificationLocation=context:/WEB-INF/Dashboard.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.Conditional pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/Conditional.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.GeneTextField pageSpecification=false specificationLocation=context:/WEB-INF/GeneTextField.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.table.components.TableValues pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/contrib/table/components/TableValues.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GenomeStats.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.Option pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/Option.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.FeatureLinksCollapsible pageSpecification=false specificationLocation=context:/WEB-INF/FeatureLinksCollapsible.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.DisplayExpressionData pageSpecification=false specificationLocation=context:/WEB-INF/DisplayExpressionData.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/ProteinInformation.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.Block pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/Block.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Credits.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.ResourceMenu pageSpecification=false specificationLocation=context:/WEB-INF/ResourceMenu.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.ContextImageInput pageSpecification=false specificationLocation=context:/WEB-INF/ContextImageInput.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Fallback.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.html.Body pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/html/Body.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.PropertySelection pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/PropertySelection.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.SearchParameterGroup pageSpecification=false specificationLocation=context:/WEB-INF/SearchParameterGroup.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.IfPageEnabled pageSpecification=false specificationLocation=context:/WEB-INF/IfPageEnabled.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.LinkSubmit pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/LinkSubmit.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.InsertReleaseProperty pageSpecification=false specificationLocation=context:/WEB-INF/InsertReleaseProperty.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/BlastOutput.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.HelpComponent pageSpecification=false specificationLocation=context:/WEB-INF/HelpComponent.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GlobalSearch.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Downloads.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.table.components.TableView pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/contrib/table/components/TableView.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.RenderBody pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/RenderBody.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.ImageSubmit pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/ImageSubmit.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneStatsDetail.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.html.InsertText pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/html/InsertText.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.AlignmentDisplay pageSpecification=false specificationLocation=context:/WEB-INF/AlignmentDisplay.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.HelpWindow pageSpecification=false specificationLocation=context:/WEB-INF/HelpWindow.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/BatchSelect.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.AssemblyFeatureCounts pageSpecification=false specificationLocation=context:/WEB-INF/AssemblyFeatureCounts.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/RegulatoryNetworkIndex.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.GeneLocus pageSpecification=false specificationLocation=context:/WEB-INF/GeneLocus.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/ViewGeneAlignment.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.IfPagePermitted pageSpecification=false specificationLocation=context:/WEB-INF/IfPagePermitted.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/TranscriptDetails.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.table.components.TableFormPages pageSpecification=false specificationLocation=context:/WEB-INF/CalhounTableFormPages.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneConfidence.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.FeatureBrowserControls pageSpecification=false specificationLocation=context:/WEB-INF/FeatureBrowserControls.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.TranscriptDisplay pageSpecification=false specificationLocation=context:/WEB-INF/TranscriptDisplay.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.html.ExceptionDisplay pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/html/ExceptionDisplay.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.RenderBlock pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/RenderBlock.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Resources.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.html.Script pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/html/Script.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/FeatureDetails.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Phenotypes.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.link.GenericLink pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/link/GenericLink.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.GenomeView pageSpecification=false specificationLocation=context:/WEB-INF/GenomeView.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.RegionActionForm pageSpecification=false specificationLocation=context:/WEB-INF/RegionActionForm.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.TableHeaderBlock pageSpecification=false specificationLocation=context:/WEB-INF/TableHeaderBlock.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.HotSpotImage pageSpecification=false specificationLocation=context:/WEB-INF/HotSpotImage.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Pfam.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.DisplayValidationError pageSpecification=false specificationLocation=context:/WEB-INF/DisplayValidationError.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.Any pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/Any.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.AssemblyRegionSelection pageSpecification=false specificationLocation=context:/WEB-INF/AssemblyRegionSelection.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.TextArea pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/TextArea.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.CommonStylesheets pageSpecification=false specificationLocation=context:/WEB-INF/CommonStylesheets.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.ReleaseAssetImage pageSpecification=false specificationLocation=context:/WEB-INF/ReleaseAssetImage.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.components.InvokeListener pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/components/InvokeListener.jwc allowBody=false allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/PolymorphismDetails.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/ToolsIndex.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.StatisticsTable pageSpecification=false specificationLocation=context:/WEB-INF/StatisticsTable.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Chromomap.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.ContextImage pageSpecification=false specificationLocation=context:/WEB-INF/ContextImage.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GeneDetails.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/FungicycLink.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/ChipSeqSearchRegulators.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/MultiDownloads.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.AnnotationSummary pageSpecification=false specificationLocation=context:/WEB-INF/AnnotationSummary.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.StaticExonTable pageSpecification=false specificationLocation=context:/WEB-INF/StaticExonTable.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.Checkbox pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/Checkbox.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/DataBrowser.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.web.component.DirectUrlGenerator pageSpecification=false specificationLocation=context:/WEB-INF/DirectUrlGenerator.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.Select pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/Select.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/Rfam.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.ProteinMap pageSpecification=false specificationLocation=context:/WEB-INF/ProteinMap.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.table.components.Table pageSpecification=false specificationLocation=context:/WEB-INF/CalhounTable.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.html.Shell pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/html/Shell.jwc allowBody=true allowInformalParameter=false]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.IfResourceEnabled pageSpecification=false specificationLocation=context:/WEB-INF/IfResourceEnabled.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/GenomeDescriptions.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/MultiHome.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.Typo3 pageSpecification=false specificationLocation=context:/WEB-INF/Typo3.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/MetabolicNetworkIndex.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.JavaScriptInitialization pageSpecification=false specificationLocation=context:/WEB-INF/JavaScriptInitialization.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.DatePicker pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/DatePicker.jwc allowBody=false allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/FeatureSearch.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.table.components.inserted.SimpleTableColumnFormComponent pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/contrib/table/components/inserted/SimpleTableColumnFormComponent.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=calhoun.external.component.DeleteIcon pageSpecification=false specificationLocation=context:/WEB-INF/DeleteIcon.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.contrib.table.components.TableRows pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/contrib/table/components/TableRows.jwc allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=null pageSpecification=true specificationLocation=context:/WEB-INF/release/SearchOntologyFlat.page allowBody=true allowInformalParameter=true]
|
|---|
| ComponentSpecification[componentClassName=org.apache.tapestry.form.TextField pageSpecification=false specificationLocation=classpath:/org/apache/tapestry/form/TextField.jwc allowBody=false allowInformalParameter=true]
|
|---|
| cached expression count | 1194 |
|---|
| cached expressions | containsRole(autocalledGeneRole)
|
|---|
| components.checkboxRenderBlock
|
|---|
| release.allAssemblies
|
|---|
| blastParameters.gapped
|
|---|
| term.name
|
|---|
| previousGene
|
|---|
| networkParams
|
|---|
| rowCount
|
|---|
| currentAssembly.id
|
|---|
| helpImage
|
|---|
| currentHit
|
|---|
| canMapCurrentAssembly
|
|---|
| coord
|
|---|
| userInstitution
|
|---|
| currentFaq.question
|
|---|
| expandIcon
|
|---|
| rankColumn
|
|---|
| hasSnpHere(components.sampleLoop1.value) and sampleHasReadData(components.sampleLoop1.value)
|
|---|
| formatter.format(currentAnnotationEdit.creationDate)
|
|---|
| familyStartMap.get(components.family.value)
|
|---|
| currentSilo.label
|
|---|
| findMutations(currentAllele).getAllele()
|
|---|
| pageFooter
|
|---|
| feature.findXrefBySource('tbdbOperonPage').externalDbUrl
|
|---|
| 'sequence' + index
|
|---|
| showDetailsIcon
|
|---|
| statsList
|
|---|
| mailSent
|
|---|
| listedAnnotation
|
|---|
| !PolyLocus.RefAllele.equals(currentAllele)
|
|---|
| term.definition
|
|---|
| allLevels.size
|
|---|
| 0
|
|---|
| hasResequencingTracks()
|
|---|
| 7
|
|---|
| getNetworkParams(target)
|
|---|
| selectAllIcon
|
|---|
| components.outline2.index > (categories.size()-1)/2
|
|---|
| levelIndex
|
|---|
| currentTopic.anchor
|
|---|
| GVLocation
|
|---|
| contentWrapperId!=null
|
|---|
| getStatsMap(components.assemblyLoop2.value)['exonGCPercent']
|
|---|
| currentAnnotationEdit.status
|
|---|
| resources.citation
|
|---|
| geneDownloadTypes.size()+1-components.dlHeadersGene.index
|
|---|
| 'Your Institution Here'
|
|---|
| pdbXrefs
|
|---|
| headerDelegate
|
|---|
| components.assemblyLoop.value.id
|
|---|
| allLevels.size + 1
|
|---|
| contentWrapperId
|
|---|
| tableName
|
|---|
| page.neighborhoodImageAsset.buildURL()
|
|---|
| page.annotations neq null and page.annotations.size gt 0
|
|---|
| statsMap.containsKey('numBpCompared') and statsMap['numBpCompared']!='0'
|
|---|
| blastParameters.program == null
|
|---|
| columnClass
|
|---|
| linkIsEmpty()
|
|---|
| emptyImage
|
|---|
| page.components.expressionData.size gt 0
|
|---|
| fileURL
|
|---|
| 'javascript:toggleDisplay(\''+currentHit.hitId+'\',false)'
|
|---|
| 'YourEmail@YourInstitution.org'
|
|---|
| numberTranslator
|
|---|
| getBioSource('ffged')
|
|---|
| page.geneNeighborhood
|
|---|
| currentHeader
|
|---|
| resources.genomeDescriptionText
|
|---|
| validationDelegate.hasErrors
|
|---|
| components.termHelpLoop.value.name
|
|---|
| page.getFunctionalCitations({'Gene Ontology'}).size() gt 0
|
|---|
| 'release/FeatureRedirect'
|
|---|
| currentTranscript
|
|---|
| blastParameters.sequences.size > 1
|
|---|
| page.title == 'Global Search'
|
|---|
| exception
|
|---|
| tableColumnRenderer
|
|---|
| listeners.doSearch
|
|---|
| asmLevelsJSArray
|
|---|
| getNestedComponent('$Border.navigation.typo3QuickSearch')
|
|---|
| currentCurationFlag.description
|
|---|
| isOperon
|
|---|
| currentTypeIndex
|
|---|
| height
|
|---|
| valueRendererOverrides
|
|---|
| ajaxListeners.getUpdateRange
|
|---|
| description
|
|---|
| page.gene.locus
|
|---|
| page.components.expressionData.size
|
|---|
| currentStrain.replaceAll(' ','_') + ' ' + alignmentSequences.get(currentStrain).sequence
|
|---|
| getHmmerHit().family.id
|
|---|
| getFastaSequences({gene}, @calhoun.bean.SequenceGeneratorType@RAW)
|
|---|
| 'background:#' + synonymousColor
|
|---|
| listeners.doSearch
|
|---|
| listeners.collapseSection
|
|---|
| getSampleName(currentStrain)
|
|---|
| blastParameters.evalue
|
|---|
| listeners.gotoRawOutput
|
|---|
| currentAssemblyIndex
|
|---|
| currentPropertyLink
|
|---|
| label
|
|---|
| { currentAllele.id, gene.id }
|
|---|
| queryTypes.asList()
|
|---|
| urlRewriter.rewriteUrl('${url.stanford}/cgi-bin/repository/repository.pl')
|
|---|
| getDbUrl()
|
|---|
| matrixModel
|
|---|
| {help.text, help.min, false}
|
|---|
| resources.multiHomeTopImage
|
|---|
| page.annotation != null or page.canEditAnnotations()
|
|---|
| itsGene
|
|---|
| page.getFilteredXrefs({'TB_IN_VIVO_TRASH'},null)
|
|---|
| beans.evenOdd.next
|
|---|
| curAspectId != 'None'
|
|---|
| release.organismClass == @calhoun.bean.AssemblyRelease$OrganismClass@UNKNOWN
|
|---|
| polyLocus.start neq polyLocus.stop
|
|---|
| pubmedUrl
|
|---|
| '>'+proteinHeader+'\n'+formattedProteinSequence
|
|---|
| gappedModel
|
|---|
| featureActionNames
|
|---|
| exon
|
|---|
| listeners.displayOntologyDetails
|
|---|
| localRuler
|
|---|
| familyColorMap.get(components.family.value)
|
|---|
| hasAnnotation
|
|---|
| nameChanged
|
|---|
| regulatorColumn
|
|---|
| 'http:[^\\s]+'
|
|---|
| fileSize
|
|---|
| listeners.doLocalCDSBlast
|
|---|
| components.header
|
|---|
| experimentsSize gt 0
|
|---|
| geneCitationMap.keySet()
|
|---|
| name
|
|---|
| seqTargetAsFrameSegment
|
|---|
| locus
|
|---|
| drawingStartAtBase
|
|---|
| addedPublications.length
|
|---|
| currentHsp
|
|---|
| currentStatKey
|
|---|
| SNPCoordinate
|
|---|
| page.getFunctionalCitations({'COG'}).size() gt 0
|
|---|
| listeners.gotoChromomap
|
|---|
| page.getFunctionalCitations({'TB Pathway'}).size()
|
|---|
| blastDatabases.get(selectedDatabaseIndex).description
|
|---|
| tracks
|
|---|
| @calhoun.external.core.release.OrthologSearch@EXCLUDE
|
|---|
| listeners.incrementSiloIndex
|
|---|
| polyLocus.aaPosition
|
|---|
| searchParameter.updatesParameters
|
|---|
| image.height
|
|---|
| broadLogo
|
|---|
| gene.length
|
|---|
| categories
|
|---|
| getFGSCUrl()
|
|---|
| 'release/GeneDetails'
|
|---|
| currentNews.headline
|
|---|
| alignmentTabData
|
|---|
| downloadParameter != null
|
|---|
| currentFaq
|
|---|
| getTransient('datasets')
|
|---|
| mapRenderer
|
|---|
| page.headerDelegate
|
|---|
| resources.pageEnabledDotplot.enabled ? listeners.showHitsOnDotplot : null
|
|---|
| genes
|
|---|
| tableClass
|
|---|
| trackRole
|
|---|
| page.countPromotedCitations
|
|---|
| currentDisplayProperty
|
|---|
| initialDotplotState
|
|---|
| currentNews.content
|
|---|
| nextGeneUrl
|
|---|
| header!=null
|
|---|
| 'GO:\\d+'
|
|---|
| theUrl == null
|
|---|
| textSearchField
|
|---|
| stopColumn
|
|---|
| currentPeak.stop
|
|---|
| components.citation.value.term.id
|
|---|
| listeners.doFeatureMap
|
|---|
| element
|
|---|
| {sequenceValidator}
|
|---|
| searchReferenceId
|
|---|
| prepopulatedText
|
|---|
| PolyLocus.UniqueAlleles
|
|---|
| {currentCitation.term.assignedId,currentCitation.publication}
|
|---|
| geneFamilyId != null
|
|---|
| currentAnnotationEdit.value
|
|---|
| queryDescription
|
|---|
| currentXref.label
|
|---|
| components.databases.index
|
|---|
| page.encodedSelfURL.contains('genome.tbdb.org')
|
|---|
| annotation.status == 'promoted'
|
|---|
| statsMap
|
|---|
| hasPromotedCitations
|
|---|
| currentCitation.term.definition
|
|---|
| formObj
|
|---|
| {featureId}
|
|---|
| urlRewriter.rewriteUrl('${url.stanford}/expressionConnection.shtml')
|
|---|
| page.getFilteredXrefs({'TARGET'},null).size() > 0
|
|---|
| ontologies
|
|---|
| listeners.acceptLicense
|
|---|
| getFilteredXrefs({'tbdb_corr_catalog'},null)
|
|---|
| currentStatistic.glossaryEntry.description
|
|---|
| {blastParameters,selectedQueryIndex}
|
|---|
| blastParameters.sequences.size > 1 ? 'margin-left:0.25in' : ''
|
|---|
| currentPeak.start
|
|---|
| selectedQueryIndex
|
|---|
| displayCounts
|
|---|
| inclusiveOperons
|
|---|
| page.getFilteredXrefs({'EMBL_STITCH'},null).size() > 0
|
|---|
| currentCategoryFaqs
|
|---|
| (getAssemblyStatistic(currentAssembly,'geneCount')!=null)&&(!(getAssemblyStatistic(currentAssembly,'geneCount').getValue().startsWith('0')))
|
|---|
| currentCitation.evidenceCodeEnum.fullName
|
|---|
| currentAllele
|
|---|
| selectionMap[components.sampleLoop.value]
|
|---|
| currentTranscript.curationFlags
|
|---|
| links
|
|---|
| components.countBlock
|
|---|
| getStatsMap(components.assemblyLoop1.value)['cdsPercentCov']
|
|---|
| userComments
|
|---|
| itsGene.locus
|
|---|
| geneTextQuery
|
|---|
| operonBrowserUrl
|
|---|
| targetColumn
|
|---|
| blastParameters.numAlignments
|
|---|
| gene.sequence.linkageGroup.name
|
|---|
| locus+(geneVersion != null?'.'+geneVersion:'')
|
|---|
| page.getFilteredXrefs({'TB_IN_VIVO_TRASH'},null).size() eq 0 and page.getFilteredXrefs({'TB_IN_VITRO_TRASH'},null).size() eq 0
|
|---|
| page.geneNeighborhood neq null
|
|---|
| currentFaq.anchor
|
|---|
| page.getFunctionalCitations({'KEGG'}).size() > 0
|
|---|
| {help.excludeList, help.includeList, false}
|
|---|
| 'summary-'+currentHit.hitId
|
|---|
| isEditingNewComment() and listedAnnotation.id eq annotation.id
|
|---|
| 'radio' + components.asmLoop.index
|
|---|
| dataExist
|
|---|
| statsAssemblies
|
|---|
| request
|
|---|
| showResults
|
|---|
| currentTarget.id
|
|---|
| exon.stop
|
|---|
| components.linkBlock.getParameter('targetId')
|
|---|
| release.primaryAssembly.organismFullName
|
|---|
| pageContentOverride
|
|---|
| featureFileAsset.buildURL()
|
|---|
| currentDisplayProperty.label
|
|---|
| resources.newsItems
|
|---|
| gene.primaryTranscript
|
|---|
| feature.transcripts
|
|---|
| components.sourceTranscripts.index != 0
|
|---|
| 'noBorder'
|
|---|
| 'BlastX'.equals(trackRole.name)
|
|---|
| getProteinLength(gene)
|
|---|
| params.frameSegment.start
|
|---|
| blastDatabases.size()>1
|
|---|
| currentCitation.term.name
|
|---|
| countMap[currentAssemblyId]
|
|---|
| { transcript.evidenceFeature.id }
|
|---|
| plasmidStatsHeadingList
|
|---|
| page.epitopes.size() gt 0
|
|---|
| dotplotListener != null
|
|---|
| currentTrackUri
|
|---|
| listeners.gotoRfamSite
|
|---|
| editorType=='boolean'
|
|---|
| getHtmlFragmentFromClasspath('tbdbMenuPublicReseq.html')
|
|---|
| footerBlock!=null
|
|---|
| page.geneFamilyId neq null and page.geneFamily.genomeCount gt 0
|
|---|
| release.formattedFullName
|
|---|
| page.userInfo.userName == null || page.userInfo.userName == 'tbdbPublicUser'
|
|---|
| addedPublications neq null and addedPublications.length eq 1
|
|---|
| getValue(currentColumn,currentRow)
|
|---|
| buildLocationString(gene)
|
|---|
| currentGene.symbol
|
|---|
| currentRow.familyId
|
|---|
| 'release/FeatureDetails'
|
|---|
| parameterId
|
|---|
| searchParameterGroup.showTextFields
|
|---|
| 'background:#' + otherMutationsColor
|
|---|
| sortImage
|
|---|
| resources.creditTopics
|
|---|
| systemPropertiesRenderer
|
|---|
| exon.strand
|
|---|
| page.targets
|
|---|
| tableModel
|
|---|
| ! last
|
|---|
| getSummaryCount(currentAssembly.id,selectedQueryIndex)
|
|---|
| getFastaSequences(@calhoun.bean.SequenceGeneratorType@RAW)
|
|---|
| currentAnnotationEdit.comment
|
|---|
| 'single'
|
|---|
| sequenceRuler
|
|---|
| params
|
|---|
| listeners.doLocalProteinBlast
|
|---|
| components.targetCell
|
|---|
| synonymsChanged
|
|---|
| selectedAssemblies
|
|---|
| transcript.curationFlags
|
|---|
| annotation != null and additionalTranscripts.size() > 0
|
|---|
| currentRowIndex
|
|---|
| familyStopMap.get(components.family.value)
|
|---|
| canDeleteAnnotations()
|
|---|
| page.getFunctionalCitations({'COG'}).size() > 0
|
|---|
| hasPendingCitations
|
|---|
| 'javascript:toggleDisplayAllForQuery(\''+selectedQuerySequence.header+'\', false)'
|
|---|
| inclusiveOperons.size() > 0
|
|---|
| showNormalPages
|
|---|
| isInForm
|
|---|
| searchBean
|
|---|
| editDate
|
|---|
| symbolChanged
|
|---|
| currentCategoryAnchor
|
|---|
| family.description
|
|---|
| href
|
|---|
| showTextFields
|
|---|
| isPolymorphicSite
|
|---|
| page.currentXref.externalDbUrl
|
|---|
| columnHeaderPairs
|
|---|
| transcript.curationFlags.size() > 0
|
|---|
| {getRangeValidator(false)}
|
|---|
| getStatsMap(components.assemblyLoop2.value)['interGeneGCPercent']
|
|---|
| getRefMutation().sampleNames
|
|---|
| components.ontologyLoop.value.description
|
|---|
| validationDelegate
|
|---|
| resources.licenseText.value.length()>0
|
|---|
| page.getFilteredXrefs({'TBSGC'},null).size() > 0
|
|---|
| {featureId,currentOverlappingTrackRole.toString()}
|
|---|
| featureId
|
|---|
| feature.findXrefBySource('EXPRN_SCOPE') neq null
|
|---|
| releaseDirectory
|
|---|
| {currentPeak.regulator,currentPeak.flowcell,currentPeak.lane, currentPeak.start, currentPeak.stop}
|
|---|
| components.regulatorRenderBlock
|
|---|
| components.types.value
|
|---|
| epitopes.size > 0 or feature.findXrefBySource('PDB_ACCESSION') neq null
|
|---|
| currentCreator
|
|---|
| displayAssemblies.{id}
|
|---|
| sequenceTranslator
|
|---|
| page.getFilteredXrefs({'TBGOOG'},null).size() > 0
|
|---|
| page.getFilteredXrefs({'TB_IN_VITRO_TRASH'},null).size() > 0
|
|---|
| currentHit.hsps
|
|---|
| page.breadcrumbPages
|
|---|
| gene.locus
|
|---|
| genomeStatsKeysList
|
|---|
| listeners.doSequence
|
|---|
| page.getFunctionalCitations({'COG'}).size()
|
|---|
| getNetworkParams(currentPeak.regulator)
|
|---|
| currentDownloadType.filenameSuffix
|
|---|
| ajaxListeners.pollStatus
|
|---|
| getFastaSequences(@calhoun.bean.SequenceGeneratorType@TRANSLATE)
|
|---|
| components.assemblyLoop.value.organismShortName
|
|---|
| currentTextId
|
|---|
| resources.mapList
|
|---|
| canEditStats
|
|---|
| currentSilo
|
|---|
| resources.multiHomeImage
|
|---|
| exception.message
|
|---|
| getAssemblyStatistic(currentAssembly,'sequencedBy').getValue()
|
|---|
| components.ontologyLoop.value.name
|
|---|
| 'Page '+currentPage+' of '+pageCount
|
|---|
| geneProductColumn
|
|---|
| currentOverlappingTrackRole
|
|---|
| titleBarBlock != null
|
|---|
| rowHeaderPairs
|
|---|
| checkboxColumn
|
|---|
| columnSelectedParameters
|
|---|
| @org.apache.commons.lang.StringUtils@join(gene.transcripts.{productName neq null ? productName : '[unnamed product]'}.iterator(), ',')
|
|---|
| 't'+currentIndex
|
|---|
| fwdPageContext
|
|---|
| parentPaths
|
|---|
| feature.stop
|
|---|
| currentAllele.identifier
|
|---|
| frameSegment.start
|
|---|
| urlRewriter.rewriteUrl('${url.stanford}/tbdbPages/login.shtml?resume='+page.encodedSelfURL)
|
|---|
| pubMedURL
|
|---|
| geneCitationMap.get(curAspectId)
|
|---|
| curatedTitle
|
|---|
| defaultTopBar
|
|---|
| hasBlastHistory
|
|---|
| otherCommunityAnnotations neq null && otherCommunityAnnotations.size > 0
|
|---|
| feature.findXrefBySource('EXPRN_SCOPE').externalDbUrl
|
|---|
| resources.mapIndexText
|
|---|
| filterModel
|
|---|
| term.ontology.name.replace(' ','_')
|
|---|
| listedAnnotation.status.equals('curated') ? 'Curated' : ''
|
|---|
| getAlignmentViewer()
|
|---|
| 'hider'+helpId
|
|---|
| showEditIcon
|
|---|
| url
|
|---|
| hitLength
|
|---|
| currentCategory.value
|
|---|
| transcript.id
|
|---|
| featureSearchService
|
|---|
| currentAnnotationEdit.comment neq null
|
|---|
| displayPage
|
|---|
| page.inclusiveOperons.size()
|
|---|
| selectionMap[currentPeak]
|
|---|
| feature.findXrefBySource('EXPRN_CNX') neq null
|
|---|
| term.aspect.displayName
|
|---|
| page.getFunctionalCitations({'NC Pathway'}).size() gt 0
|
|---|
| currentColumn
|
|---|
| sampleNames
|
|---|
| editorType=='date'
|
|---|
| currentCitation.term.id
|
|---|
| transcript.evidenceFeature != null
|
|---|
| submitListener
|
|---|
| 'select'+label
|
|---|
| exception.stackTrace
|
|---|
| { currentAllele.id, currentGene.id }
|
|---|
| 'Your Name Here'
|
|---|
| canCurateListedAnnotation() and not isEditing and not (state.annotation != null and state.annotation.id eq listedAnnotation.id)
|
|---|
| pendingTitle
|
|---|
| geneSynonyms
|
|---|
| jsonTranscriptStructure
|
|---|
| drugResistance
|
|---|
| 'javascript:help_show('+components.ontologyLoop.index+');'
|
|---|
| listeners.hideIntrons
|
|---|
| topLevelBlock != null
|
|---|
| resources.adhocMapDownloads
|
|---|
| displayName
|
|---|
| bestHsp.length
|
|---|
| 'detail-'+currentHit.hitId
|
|---|
| currentAnnotationEdit
|
|---|
| renderBody
|
|---|
| components.family.value.id
|
|---|
| form.name
|
|---|
| currentXref
|
|---|
| columnSpan > 2 ? columnSpan : 2
|
|---|
| '#'+currentCategoryAnchor
|
|---|
| displayProperties
|
|---|
| searchState
|
|---|
| !hasAnnotation && !isAnnotation
|
|---|
| columnHeaderPairs[currentColumn][0]
|
|---|
| polyLocus.gene.locus + ' - ' + polyLocus.gene.name
|
|---|
| components.sampleLoop.value
|
|---|
| currentAdhocAsset.description
|
|---|
| page.requestCycle.listenerParameters
|
|---|
| identifier
|
|---|
| segments
|
|---|
| new java.lang.Double(averageIdentity*100).intValue()
|
|---|
| {term.assignedId}
|
|---|
| resultString
|
|---|
| bestHsp.bitScore
|
|---|
| hotSpotUrlSource
|
|---|
| term.obsolete
|
|---|
| currentCitation.evidenceCodeEnum
|
|---|
| valueClass
|
|---|
| page.getFilteredXrefs({'TARGET'},null)
|
|---|
| components.geneSymbolRenderBlock
|
|---|
| getFilteredXrefs({'tbdb_scatterplot'},null)
|
|---|
| submitAction
|
|---|
| previousGeneUrl
|
|---|
| currentCurationFlag
|
|---|
| start
|
|---|
| bestHsp.evalue
|
|---|
| nextGene.id
|
|---|
| {help.includeList, help.excludeList, true}
|
|---|
| currentRow.familyName
|
|---|
| page.getFunctionalCitations({'TB Pathway'}).size() > 0
|
|---|
| listeners.displayGenes
|
|---|
| drugResistance.length neq 0
|
|---|
| hierarchyMap
|
|---|
| currentPageTitle
|
|---|
| components.regionActionForm.id
|
|---|
| returnURL
|
|---|
| !(isLoggedOn())
|
|---|
| getStatsMap(components.assemblyLoop1.value)['interGeneLengthMean']
|
|---|
| pfamEntriesForLetter
|
|---|
| (assemblyStatsHeadingList+','+plasmidStatsHeadingList)
|
|---|
| showLabels
|
|---|
| annotationEditSource
|
|---|
| annotationGene != null
|
|---|
| gBOrfFile
|
|---|
| validator
|
|---|
| mutationType
|
|---|
| block
|
|---|
| allLevels
|
|---|
| components.children.value.id
|
|---|
| familyColorMap.keySet()
|
|---|
| currentSilo.helpText neq null
|
|---|
| warning != null
|
|---|
| listeners.expandSection
|
|---|
| components.featureActionForm.id
|
|---|
| initialSortOrder
|
|---|
| displayTopBar
|
|---|
| exceptions
|
|---|
| getRefMutation().getNumberOfStrains()
|
|---|
| currentOverlappingTrackRole.displayName
|
|---|
| firstTranscriptStart
|
|---|
| currentLink.shortLabel.replaceAll(' ',' ')
|
|---|
| UniqueAlleles != null ? @calhoun.external.search.FeatureSearchConfig@removeBrackets(UniqueAlleles.toString()) : ''
|
|---|
| jsonAssemblyStructure
|
|---|
| currentGene.primaryTranscript.productName
|
|---|
| startColumn
|
|---|
| 'http://www.tbdb.org/expressionHistory.shtml?gn=' + page.gene.locus
|
|---|
| selectedBlastResults != null && selectedBlastResults.hits != null && selectedBlastResults.hits.size() > 0
|
|---|
| assemblyHasChromosomes
|
|---|
| defaultTableSessionStateManager
|
|---|
| getStatistic(currentStatKey)!=null
|
|---|
| isGene()
|
|---|
| hasFunctionalCitations()
|
|---|
| feature.findXrefBySource('tbdb_scatterplot').externalDbUrl
|
|---|
| adapterFactory.getRenderableAdaptor(property.value)
|
|---|
| currentAssemblyId
|
|---|
| showRange
|
|---|
| countMap.keySet()
|
|---|
| 'javascript:setAll(1)'
|
|---|
| transcript.evidenceFeature.name !=null
|
|---|
| page.getFunctionalCitations({'Gene Ontology'})
|
|---|
| page.jsonExpressionData
|
|---|
| components.transcripts.value
|
|---|
| 'background:#' + nonSynonymousColor
|
|---|
| term neq null
|
|---|
| '.zip'
|
|---|
| GVConfigFile
|
|---|
| exception.exceptionClassName
|
|---|
| family.gatheringCutoff
|
|---|
| treeFileAsset neq null
|
|---|
| 'javascript:toggleDisplay(\''+currentHit.hitId+'\',true)'
|
|---|
| currentTargetGeneDescription
|
|---|
| geneDownloadTypes.size() > 0
|
|---|
| viewerApplet.buildURL()
|
|---|
| hasVisibleParameters
|
|---|
| frameSegment.stop
|
|---|
| allowGeneSearch
|
|---|
| getAssemblyStatistic(currentAssembly,'sequencedBy').getValue().contains('Broad')
|
|---|
| currentCheckbox
|
|---|
| unselectAllIcon
|
|---|
| resources.infoTopics
|
|---|
| tableRow
|
|---|
| genomeStatsHeaderList
|
|---|
| 'tr'
|
|---|
| startFileUrl
|
|---|
| annotation != null or canEditAnnotations()
|
|---|
| silosByCategory.entrySet()
|
|---|
| term.aspect != null
|
|---|
| page.getFunctionalCitations({'TB Reaction'})
|
|---|
| controller != null and controller.state.failureMessage != null
|
|---|
| 'Your comments here.'
|
|---|
| currentCitation.term.assignedId
|
|---|
| getResidues()
|
|---|
| components.parents.value.id
|
|---|
| lowercaseTranslator
|
|---|
| page.geneFamily.genomeCount
|
|---|
| currentGene != null
|
|---|
| components.publication.value
|
|---|
| getFastaSequences(gene.transcripts, @calhoun.bean.SequenceGeneratorType@CDS)
|
|---|
| citation.pubMedId neq null
|
|---|
| family.name
|
|---|
| transcript.length
|
|---|
| components.family.value.description
|
|---|
| userName
|
|---|
| params.frameSegment
|
|---|
| drawingStopAtBase
|
|---|
| fileDate
|
|---|
| password
|
|---|
| parameters
|
|---|
| page.getFilteredXrefs({'TB_IN_VITRO_TRASH'},null)
|
|---|
| queryDescription != null
|
|---|
| listeners.doGeneSearch
|
|---|
| {'$id'}
|
|---|
| cssClass
|
|---|
| 'javascript:deselect(' + levelIndex + ')'
|
|---|
| components.alleleLinkBlock
|
|---|
| listeners.gotoRegion
|
|---|
| chipSeqPeaks
|
|---|
| geneHasPolyLocus(featureId)
|
|---|
| 'toggleDisplay(\''+currentHit.hitId+'\',showDetail);'
|
|---|
| searchService
|
|---|
| reportStatusRenderer
|
|---|
| findMutations(currentAllele) neq null
|
|---|
| resourceExists(resourceFileName)
|
|---|
| tableIndex
|
|---|
| feature.findXrefBySource('tbdb_scatterplot') neq null
|
|---|
| polyLocus.gene.strand.isPlus()
|
|---|
| components.geneProductRenderBlock
|
|---|
| trackRoleOverlaps.asList()
|
|---|
| page.proteinDomain
|
|---|
| xrefs.size()>0
|
|---|
| listeners.searchGenes
|
|---|
| searchParameterGroup.showRange
|
|---|
| trackRoleOverlaps.size() > 0
|
|---|
| @calhoun.external.core.release.OrthologSearch@INCLUDE
|
|---|
| lastPageContext
|
|---|
| citationsChanged
|
|---|
| components.searchForm.searchBean.getParameter(@calhoun.external.search.OrthologSearchService@ASM_COUNT_FIELD).value
|
|---|
| page.domainAsset.buildURL()
|
|---|
| selectionModel
|
|---|
| gene.geneVersion != null
|
|---|
| @calhoun.bean.Aspect@fromName(curAspectId).displayName
|
|---|
| transcript.exons
|
|---|
| trackRoleOverlaps.get(currentOverlappingTrackRole)
|
|---|
| tRNAFile
|
|---|
| citation.publication
|
|---|
| transcript.start
|
|---|
| page.visibleAlleles neq null and page.visibleAlleles.size gt 0
|
|---|
| isEpitope ? false : true
|
|---|
| getFilteredXrefs({'EXPRN_SCOPE'},null)
|
|---|
| currentCategoryLinkLabel
|
|---|
| target
|
|---|
| 'inline-help'+helpId
|
|---|
| assemblyStatsKeyList
|
|---|
| assemblyStatsHeadingList
|
|---|
| polyLocusList.size() > 0
|
|---|
| currentTargetSequenceDescription
|
|---|
| argoCookie
|
|---|
| baseUrl
|
|---|
| !condBack
|
|---|
| polyLocus.start
|
|---|
| blastParameters.numDescriptions
|
|---|
| request.getSession(false) != null
|
|---|
| currentIndex
|
|---|
| oldName
|
|---|
| page.components.ajaxCall
|
|---|
| {annotation.sourceGene.id, annotation.id}
|
|---|
| pageSize
|
|---|
| image
|
|---|
| isSorted
|
|---|
| components.targetRef
|
|---|
| downloadTypesForSequence.size()+1-components.dlHeadersAssembly.index
|
|---|
| help.getHierarchyNameString(help.exampleFrameSegment)
|
|---|
| startPageParams
|
|---|
| getAssemblyStatistic(currentAssembly,'sequencedBy')!=null
|
|---|
| header
|
|---|
| featureAction
|
|---|
| description neq null and description.length() gt 0
|
|---|
| (hasFunctionalCitations() && (functionalCitations.size() > 0))||(inclusiveOperons.size() > 0)
|
|---|
| @java.lang.String@format('%10.1f',{score}.toArray())
|
|---|
| selectionStart
|
|---|
| 400
|
|---|
| page.getFilteredXrefs({'PDB_ACCESSION'},null).size()
|
|---|
| bestHsp.numIdentities
|
|---|
| currentAdhocAsset.filename
|
|---|
| separator
|
|---|
| 'basic'
|
|---|
| hasSnpHere(components.sampleLoop.value) and sampleHasReadData(components.sampleLoop.value)
|
|---|
| 'global/argo/Bootstrap'
|
|---|
| page.getFunctionalCitations({'TB Reaction'}).size()
|
|---|
| featureRole.displayName
|
|---|
| currentCitation
|
|---|
| page.hasPromotedCitations
|
|---|
| currentAnnotationEdit.id
|
|---|
| summaryColumnPairs
|
|---|
| displayPageContext
|
|---|
| currentPng
|
|---|
| jsonExpressionData
|
|---|
| sequence.group.narrow()[0].organismShortName + ': ' +(#seqName = sequence.group.narrow()[0].sequenceLevel.toString(), #seqName == 'Genome' ? '' : #seqName +' '+sequence.groupOrder+': ') + start+'-'+stop+' '+strand
|
|---|
| findMutations(currentAllele).getMutation(currentAllele)
|
|---|
| listenerParams
|
|---|
| rankFormatter.format(currentPeak.rank)
|
|---|
| page.releasePage && page.allowResourceEditing
|
|---|
| getStatsMap(components.assemblyLoop2.value)['cdsGCPercent']
|
|---|
| regionActionNames
|
|---|
| nextGene != null
|
|---|
| headerBlock!=null
|
|---|
| tableColumn
|
|---|
| blastDatabases
|
|---|
| getGeneCount(components.assemblyLoop.value,components.termLoop.value)
|
|---|
| itsGene neq null
|
|---|
| imageAsset
|
|---|
| dreamDbUrl
|
|---|
| 'text'+label
|
|---|
| page.includeGoogleTracking
|
|---|
| useLocusLink
|
|---|
| countsByAssembly
|
|---|
| selectedQuerySequence.header
|
|---|
| geneDownloadTypes
|
|---|
| canEditAnnotations() and not isEditingComment()
|
|---|
| currentNews.date
|
|---|
| dnaSequences
|
|---|
| page.getFunctionalCitations({'TB Pathway'}).size() gt 0
|
|---|
| page.getFunctionalCitations({'NC Reaction'}).size() gt 0
|
|---|
| resequencingEnabled
|
|---|
| currentStrain
|
|---|
| components.rankRenderBlock
|
|---|
| listeners.doAlignmentViewer
|
|---|
| term.selectParentTerms('is_a')
|
|---|
| components.genes.value
|
|---|
| geneLocus
|
|---|
| tableRowsIterator
|
|---|
| currentSilo.helpText
|
|---|
| validatorMap
|
|---|
| exon.length
|
|---|
| components.bioSourceLinkBlock
|
|---|
| components.ontologyLoop.index == 0
|
|---|
| property.name
|
|---|
| querySeq.gi
|
|---|
| insertStringAt(curSegment.retrieveRawSequence(), '\n', 100)
|
|---|
| maxExpected
|
|---|
| page.currentXref.label
|
|---|
| flowcellColumn
|
|---|
| getStatsMap(components.assemblyLoop2.value)['intronGCPercent']
|
|---|
| 'explain('+ explain +');'
|
|---|
| page.hasUncategorizedCitations(page.gene)
|
|---|
| page.getFunctionalCitations({'Gene Ontology'}).size()
|
|---|
| editable
|
|---|
| gene.id
|
|---|
| otherCommunityAnnotations
|
|---|
| currentDownloadType
|
|---|
| urlRewriter.rewriteUrl('${url.stanford}/geneExpressionScope.shtml')
|
|---|
| page.getFunctionalCitations({'KEGG'})
|
|---|
| currentNews
|
|---|
| pageHeader != null
|
|---|
| components.publication.index>0
|
|---|
| page.release.featureTrackRoles
|
|---|
| resources.projectDescription
|
|---|
| page.getFilteredXrefs({'myco_protease'},null).size() > 0
|
|---|
| isMultiple
|
|---|
| {featureId,featureTrackRole.toString()}
|
|---|
| isOperon()
|
|---|
| transcript
|
|---|
| experimentsSize
|
|---|
| headerBlock
|
|---|
| addedPublications neq null and addedPublications.length gt 1
|
|---|
| userEmail
|
|---|
| release.formattedShortName
|
|---|
| canViewCollaboratorDownloads()
|
|---|
| treeFileAsset.buildURL()
|
|---|
| containsRole(blastXRole)
|
|---|
| resources.fundingAgency.value.equals("NIAID")
|
|---|
| uncategorizedCitations(gene)
|
|---|
| {'Feature Type','Name','Text Search'}
|
|---|
| {feature.id, getFeatureTrackRole()}
|
|---|
| currentPropertyValue neq null and !currentPropertyValue.equals('')
|
|---|
| feature.findXrefBySource('tbdb_corr_catalog') neq null
|
|---|
| 'JsonArray'+levelIndex
|
|---|
| components.databases.value.description neq ''
|
|---|
| jsonFeaturesStructure
|
|---|
| editorType=='region'
|
|---|
| hasUncategorizedCitations(gene) or ( annotation neq null and hasUncategorizedCitations(annotation.annotationGene) )
|
|---|
| page.getFilteredXrefs({'TB_IN_VIVO_TRASH'},null).size() > 0
|
|---|
| condCurrent
|
|---|
| lastTranscriptStop
|
|---|
| 'usemap'
|
|---|
| compressionSuffix
|
|---|
| page.getFilteredXrefs({'EMBL_STRING'},null)
|
|---|
| rFAMFile
|
|---|
| altLabel
|
|---|
| page.getFilteredXrefs({'2DPAGE'},null).size() > 0
|
|---|
| message
|
|---|
| release.organismClass == @calhoun.bean.AssemblyRelease$OrganismClass@VIRUSES
|
|---|
| resultsFilter
|
|---|
| findMutations(polyLocus.refAllele).getAllele()
|
|---|
| help.includeListNames
|
|---|
| asmDestiny[curAssembly]
|
|---|
| currentTopic.answer
|
|---|
| annotation != null
|
|---|
| polyLocus.gene!=null
|
|---|
| components.genes.value.getName()
|
|---|
| currentLabel
|
|---|
| page.regulators gt 0
|
|---|
| regionAction
|
|---|
| score
|
|---|
| selectedDatabaseIndex
|
|---|
| displayAssemblies
|
|---|
| collapseIcon
|
|---|
| currentAdhocAsset
|
|---|
| !showIntrons
|
|---|
| snpLocation
|
|---|
| getStatsMap(components.assemblyLoop1.value)['geneCount']
|
|---|
| params.selectedTracks[trackRole]
|
|---|
| inclusiveOperons != null
|
|---|
| overlappingManualEdits neq null && overlappingManualEdits.size() > 0
|
|---|
| {gene.id}
|
|---|
| page.geneProfiles
|
|---|
| params.blastScore
|
|---|
| gene
|
|---|
| 'http://www.broadinstitute.org/annotation/tbdb.org/diversityGraph/stats_'+gene.locus+'.js'
|
|---|
| hasPolymorphisms
|
|---|
| searchParameter.value
|
|---|
| !resources.multiHomeTopImage.enabled
|
|---|
| components.citation.value.evidenceCodeEnum
|
|---|
| components.assemblyLoop1.value.organismShortName
|
|---|
| networkParams neq null
|
|---|
| geneHistory
|
|---|
| evalueModel
|
|---|
| jnlpParameters
|
|---|
| polyLocus.gene neq null
|
|---|
| currentAssembly
|
|---|
| transcript.splicedLength
|
|---|
| searchParameter.label
|
|---|
| currentPropertyValue
|
|---|
| startPageName
|
|---|
| components.flowcellRenderBlock
|
|---|
| feature.sequence.linkageGroup!=null
|
|---|
| 'Specified Gene'
|
|---|
| {@calhoun.external.search.OrthologSearchService@TEXT_SEARCH_FIELD}
|
|---|
| geneFamilyId
|
|---|
| pageResource.content
|
|---|
| page.browserTitle
|
|---|
| isSnp()
|
|---|
| nextGene neq null
|
|---|
| currentCategory
|
|---|
| components.peptide.value
|
|---|
| components.citation.value
|
|---|
| src
|
|---|
| fastaFile
|
|---|
| null
|
|---|
| feature.findXrefBySource('PDB_ACCESSION') neq null
|
|---|
| 'GenomeDescriptions.html#'+currentAssembly.id
|
|---|
| sequences
|
|---|
| true
|
|---|
| page.getFunctionalCitations({'Functional Catalogue'})
|
|---|
| getTransient('textMatchFields')
|
|---|
| visibleAlleles.size() > 0
|
|---|
| {@calhoun.external.search.OrthologSearchService@UNAMBIGUOUS_FIELD}
|
|---|
| components.parentPath.value.id
|
|---|
| globalSearchUrl
|
|---|
| gene.sequence.linkageGroup!=null
|
|---|
| page.getFilteredXrefs({'EMBL_STRING'},null).size() > 0
|
|---|
| wrappedAssemblyBean
|
|---|
| hideDetailsIcon
|
|---|
| 'title' + levelIndex
|
|---|
| buildDate
|
|---|
| findMutations(currentAllele).getNumberOfStrains()
|
|---|
| selectedHits
|
|---|
| searchParameterGroup.showLabels
|
|---|
| family.source.id
|
|---|
| listeners.selectAssembly
|
|---|
| useHmmrLink
|
|---|
| term.definition neq null
|
|---|
| last
|
|---|
| ''+components.ontologyLoop.index
|
|---|
| page.listeners.gotoLogin
|
|---|
| !resourceListIsEmpty('adhocSNPDownloads')
|
|---|
| components.termHeaderLoop.value.name
|
|---|
| annotation.id
|
|---|
| feature.findXrefBySource('tbdb_corr_catalog').externalDbUrl
|
|---|
| level
|
|---|
| components.heightRenderBlock
|
|---|
| page.gene.transcripts.size
|
|---|
| {components.assemblyLoop.value.id,components.termLoop.value.id}
|
|---|
| components.startRenderBlock
|
|---|
| 'javascript:loadGV(\'' + getPolyfileUrl(components.sampleLoop.value) + '\');javascript:loadGV(\'' + getBamfileUrl(components.sampleLoop.value) + '\');'
|
|---|
| components.alleles.index > 0
|
|---|
| currentCategoryLink
|
|---|
| currentPeak.height
|
|---|
| getFastaSequences(gene.transcripts, @calhoun.bean.SequenceGeneratorType@TRANSLATE)
|
|---|
| page.getFunctionalCitations({'NC Reaction'})
|
|---|
| (genomeStatsKeysList+','+assemblyStatsKeyList+','+plasmidStatsKeyList)
|
|---|
| page.polyLocusList.size() gt 0
|
|---|
| collapsed
|
|---|
| selectionStop
|
|---|
| listeners.doBlast
|
|---|
| pageContentOverride == null
|
|---|
| @calhoun.web.util.JsonUtil@toJsonString(@calhoun.external.page.RegionSearchPage@buildRegionHash(getCurRegions(levelIndex).values()))
|
|---|
| page.goSize
|
|---|
| curAssembly.organismShortName
|
|---|
| components.familyBlock
|
|---|
| activator
|
|---|
| page.significantExpressionData neq null ? page.significantExpressionData.size : '0'
|
|---|
| hitTextSearchLimit
|
|---|
| distanceToGeneStartColumn
|
|---|
| pageList
|
|---|
| components.stopRenderBlock
|
|---|
| message!=null
|
|---|
| 'Nucleotide'
|
|---|
| components.sourceTranscripts.index == 0
|
|---|
| page.releasePage && displayNavigation
|
|---|
| 'javascript:toggleDisplayAllForQuery(\''+selectedQuerySequence.header+'\', true)'
|
|---|
| '>'+cdsHeader+'\n'+formattedCds
|
|---|
| {currentDownloadType}
|
|---|
| term.comment
|
|---|
| release.organismClass == @calhoun.bean.AssemblyRelease$OrganismClass@BACTERIA
|
|---|
| page.getFunctionalCitations({'TB Reaction'}).size() > 0
|
|---|
| id
|
|---|
| {currentAssembly.id}
|
|---|
| isGene
|
|---|
| totalCount
|
|---|
| activeCommunityAnnotations.{id}
|
|---|
| currentAssembly.organismShortName
|
|---|
| searchBean.getParameter(currentLabel)
|
|---|
| supercontigDiagram
|
|---|
| gene.transcripts
|
|---|
| resources.pageEnabledChromomap.enabled ? listeners.showHitsOnChromomap : null
|
|---|
| '<h1>'+title+'</h1>'
|
|---|
| page.regulators
|
|---|
| 'background:#' + intronicRegionColor
|
|---|
| feature.findXrefBySource('EXPRN_CNX').externalDbUrl
|
|---|
| trackRole.displayName
|
|---|
| { currentFeature.id }
|
|---|
| annotation != null ? gene.transcripts.size()*2 : gene.transcripts.size()
|
|---|
| request.getSession(false)
|
|---|
| resources.externalLinks
|
|---|
| curAssembly
|
|---|
| levelIndex==0 ? 'regions-expandingbox' : 'regions-box'
|
|---|
| 'http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed&cmd=search&term=' + citation.pubMedId
|
|---|
| -1
|
|---|
| showLinks
|
|---|
| columnRendererOverrides
|
|---|
| page.getFunctionalCitations({'NC Pathway'})
|
|---|
| isCommunityAnnotation
|
|---|
| isEpitope
|
|---|
| currentPage
|
|---|
| nextGene.locus
|
|---|
| editorType=='number'
|
|---|
| transcript.productName ? transcript.productName : '[unnamed product]'
|
|---|
| confidenceAssemblies.size() > 0
|
|---|
| fileURL neq null
|
|---|
| searchParameter.label=='Text Search'
|
|---|
| page.significantExpressionData neq null
|
|---|
| strand
|
|---|
| currentTopic.question
|
|---|
| getFilteredXrefs({'TbExpression'},null).size() > 0
|
|---|
| components.operons.value
|
|---|
| {required}
|
|---|
| getTransient('textScore')
|
|---|
| gene.locus
|
|---|
| curSegment
|
|---|
| nextGene
|
|---|
| page.getFunctionalCitations({'NC Pathway'}).size() > 0
|
|---|
| listeners.showIntrons
|
|---|
| pageHeader
|
|---|
| columnSorted
|
|---|
| {geneFamilyId, gene.id}
|
|---|
| 'javascript:multiOptions(\'BL\',\'Local BLAST with Protein Sequence|'+localProteinBlastURL+'\',\'Local BLAST with Coding Sequence|'+localCDSBlastURL+'\',\'NCBI BLAST with Protein Sequence|javascript:document.forms.ncbi_blast_protein.submit()\',\'NCBI BLAST with Coding Sequence|javascript:document.forms.ncbi_blast_cds.submit()\');'
|
|---|
| 40
|
|---|
| headingList
|
|---|
| getStatsMap(components.assemblyLoop1.value)['exonCount']
|
|---|
| getTerms(components.ontologyLoop.value)
|
|---|
| getCodingCoord(getPolyLocus())
|
|---|
| previousGene.id
|
|---|
| !release.isMultiAssemblyRelease()
|
|---|
| previousGene.locus
|
|---|
| currentTranscript.curationFlags.size()> 0
|
|---|
| transcript.evidenceFeature.name
|
|---|
| tableColumnIterator
|
|---|
| templateTag
|
|---|
| 30
|
|---|
| page.inclusiveOperons.size() gt 0
|
|---|
| currentPeak.regulator
|
|---|
| listener!=null
|
|---|
| image.width
|
|---|
| components.assemblyLoop2.value.organismShortName
|
|---|
| queryTypes[components.types.value]
|
|---|
| resources.adhocSupplementaryDownloads
|
|---|
| currentLink.url
|
|---|
| !condFwd
|
|---|
| currentPdbXref
|
|---|
| getStatsMap(components.assemblyLoop2.value)['geneGCPercent']
|
|---|
| page.geneProfiles neq '0'
|
|---|
| ' - ' + polyLocus.stop
|
|---|
| indicatorImage
|
|---|
| help.min
|
|---|
| editorType=='string'
|
|---|
| frameSegment
|
|---|
| page.getFunctionalCitations({'TB Pathway'})
|
|---|
| currentTopic
|
|---|
| currentTargetType=='transcript'
|
|---|
| @calhoun.external.util.WebUtils@toMultiLine(transcript.translate(), 100)
|
|---|
| {wrappedAssemblyBean,'feature'}
|
|---|
| page.getFunctionalCitations({'TB Reaction'}).size() gt 0
|
|---|
| help.text
|
|---|
| exon.start
|
|---|
| currentDownloadType.dataExists(release,currentAssembly)
|
|---|
| exception.properties
|
|---|
| queryStatusId
|
|---|
| columnModel
|
|---|
| components.parentPaths.value
|
|---|
| !collapsed
|
|---|
| listedAnnotation.user.userName
|
|---|
| !page.userLoggedIn
|
|---|
| genomeMapState
|
|---|
| featureMapImage
|
|---|
| page.getFunctionalCitations({'NC Pathway'}).size()
|
|---|
| getFastaSequences( @calhoun.bean.SequenceGeneratorType@CDS)
|
|---|
| currentCitation.evidenceCodeEnum neq null
|
|---|
| transcriptsChanged
|
|---|
| heightColumn
|
|---|
| linkColumn
|
|---|
| getTransient('samples')
|
|---|
| bestHsp.numPositives
|
|---|
| treeData
|
|---|
| page.annotations.size
|
|---|
| release.organismClass == @calhoun.bean.AssemblyRelease$OrganismClass@FUNGI
|
|---|
| userName
|
|---|
| index
|
|---|
| currentPublication
|
|---|
| components.curationFlag.value.description
|
|---|
| labels
|
|---|
| width
|
|---|
| gene.symbol
|
|---|
| currentTrack
|
|---|
| currentFeatureLinkLabel
|
|---|
| urlRewriter.rewriteUrl('${url.stanford}/publication.shtml?q=*&perpage=100')
|
|---|
| currentPeak
|
|---|
| feature.findXrefBySource('tbdbOperonPage') neq null
|
|---|
| @calhoun.external.search.FeatureSearchConfig@enumSetToString(mutationClasses)
|
|---|
| currentLink
|
|---|
| help.getHierarchyNameString(help.firstAssembly)
|
|---|
| currentCitation
|
|---|
| errorMsg neq null
|
|---|
| 'javascript:help_hide('+helpId+');'
|
|---|
| page.formattedTitle
|
|---|
| transcript.stop
|
|---|
| 'background:#' + intronicFeatureColor
|
|---|
| blastParameters.filter
|
|---|
| page.polyLocusList.size()
|
|---|
| strandModel
|
|---|
| components.databases.value.description
|
|---|
| searchIcon
|
|---|
| @org.apache.commons.lang.StringUtils@join(gene.synonyms.iterator(), ',')
|
|---|
| {null}
|
|---|
| page.getFilteredXrefs({'EMBL_STITCH'},null)
|
|---|
| page.visibleAlleles.size
|
|---|
| (!(locked)&&canEditGlossary)
|
|---|
| renderBody
|
|---|
| addedPublications
|
|---|
| hasUncategorizedCitations(gene)
|
|---|
| jnlpUrl
|
|---|
| '$id'
|
|---|
| rowHeader
|
|---|
| page.proteinDomain neq null
|
|---|
| components.citation.value.term.name
|
|---|
| initialSortColumn
|
|---|
| page.newElementId()
|
|---|
| 'query' + (selectedQueryIndex - -1)
|
|---|
| className
|
|---|
| page.getFilteredXrefs({'TBLIST'},null)
|
|---|
| newName
|
|---|
| imageClass
|
|---|
| mailError
|
|---|
| googleChartURL
|
|---|
| page.getFilteredXrefs({'PDB_ACCESSION'},null).size() gt 0
|
|---|
| page.getFunctionalCitations({'NC Reaction'}).size() > 0
|
|---|
| jsonPolymorphismsStructure
|
|---|
| addedTerms neq null
|
|---|
| searchParameter.model.entryLength
|
|---|
| release.permissionsAssembly.acceptedGeneCalls eq gene.analysisRun
|
|---|
| page.getFunctionalCitations({'COG'})
|
|---|
| familyDescription
|
|---|
| geneFamily.description
|
|---|
| page.getFilteredXrefs({'TBGOOG'},null)
|
|---|
| trace
|
|---|
| resources.adhocUnplacedReadsDownloads
|
|---|
| blastParameters.matrix
|
|---|
| tableModel.pageCount > 1
|
|---|
| hasGeneFamilyData()
|
|---|
| {getRangeValidator(true)}
|
|---|
| components.linkRenderBlock
|
|---|
| listeners.retrieveAlignment
|
|---|
| listeners.apply
|
|---|
| getStatsMap(components.assemblyLoop2.value)['scaffoldGCPercent']
|
|---|
| blastParameters.program
|
|---|
| tableValueRenderer
|
|---|
| { transcript.id }
|
|---|
| previousGene != null
|
|---|
| gene.curationFlags.size()>0
|
|---|
| ((!(locked))&&canEditStats)
|
|---|
| currentCategory.key
|
|---|
| downloadIcon
|
|---|
| asmDestiny.keySet()
|
|---|
| geneSymbolColumn
|
|---|
| page.getFunctionalCitations({'NC Reaction'}).size()
|
|---|
| rowHeaderPairs[currentRow][0]
|
|---|
| wasCalled
|
|---|
| hasAnnotation && !isAnnotation
|
|---|
| annotations
|
|---|
| (assemblyStatsKeyList+','+plasmidStatsKeyList)
|
|---|
| getFilteredXrefs({'EXPRN_CNX'},null)
|
|---|
| currentPropertyLink==null
|
|---|
| globalFrameId
|
|---|
| page.currentXref
|
|---|
| blastXRankSelectionModel
|
|---|
| page
|
|---|
| false
|
|---|
| displayingSequence
|
|---|
| pageFooter != null
|
|---|
| currentTargetType=='seq'
|
|---|
| getRangeTranslator(false)
|
|---|
| findMutations(currentAllele).getMutationClass()
|
|---|
| addedTerms
|
|---|
| polyLocusList.size() gt 0
|
|---|
| page.listeners.framesByText
|
|---|
| synonymCommaList
|
|---|
| blastParameters.sequences
|
|---|
| help.excludeListNames
|
|---|
| params.blastRank
|
|---|
| distanceToStartCodon
|
|---|
| retrieveAlignmentParams
|
|---|
| term.name
|
|---|
| selectedRegion
|
|---|
| 'td'+levelIndex
|
|---|
| queryTypes[blastParameters.program]
|
|---|
| page.targets gt 0
|
|---|
| fieldSize
|
|---|
| container
|
|---|
| transcript.translate().length()
|
|---|
| customHeaderBlock.block
|
|---|
| components.featureLinkBlock
|
|---|
| ! isLicenseNecessary()
|
|---|
| curStyle
|
|---|
| page.releasePage
|
|---|
| urlSource
|
|---|
| currentLink.targetPage
|
|---|
| selectedAssemblyId == null || selectedAssemblyId == currentAssembly.id
|
|---|
| currentFaq.answer
|
|---|
| new calhoun.web.util.OrderedMapSelectionModel(components.searchForm.searchBean.getParameter(@calhoun.external.search.OrthologSearchService@ASM_COUNT_FIELD).model.map)
|
|---|
| newElementId()
|
|---|
| sequenceUri
|
|---|
| gene.name
|
|---|
| allStrains
|
|---|
| title
|
|---|
| { polyLocus.gene.id }
|
|---|
| currentAnnotationEdit.property
|
|---|
| trackRoleColor
|
|---|
| visibleAlleles
|
|---|
| geneId
|
|---|
| objectId
|
|---|
| length
|
|---|
| editorType=='map'
|
|---|
| currentXref.externalDbUrl
|
|---|
| querySeq.description
|
|---|
| rewriteUrl(currentSilo.navigationUrl)
|
|---|
| annotations.size() > 0
|
|---|
| isHmmerHit && currentDisplayProperty.label == 'Family Name'
|
|---|
| isEst
|
|---|
| 'javascript:setAll(0)'
|
|---|
| isTermType('TBRXN:')
|
|---|
| @calhoun.external.core.release.OrthologSearch@DONT_CARE
|
|---|
| curAspectId
|
|---|
| components.tableHeaderBlock
|
|---|
| fileImage
|
|---|
| components.outline1.index <= (categories.size()-1)/2
|
|---|
| currentRow.geneCount
|
|---|
| listedAnnotation.comments
|
|---|
| hasAnnotation?2:1
|
|---|
| "outputtable"
|
|---|
| 'javascript:setAll(2)'
|
|---|
| altText
|
|---|
| confidenceAssemblies
|
|---|
| term.ontology.id
|
|---|
| getStatistic(currentStatKey).getFormattedValue()
|
|---|
| wrappedSearchBean
|
|---|
| page.getFilteredXrefs({'TBLIST'},null).size() > 0
|
|---|
| family.accession
|
|---|
| epitopes.size > 0
|
|---|
| selectedAssemblyId
|
|---|
| gene.geneVersion
|
|---|
| components.linkBlock
|
|---|
| alignmentSequences.keys
|
|---|
| ''+queryStart+'-'+queryStop
|
|---|
| downloadTypesForSequence
|
|---|
| findMutations(currentAllele).getResidue(currentAllele)
|
|---|
| validators
|
|---|
| new org.apache.tapestry.valid.ValidationDelegate()
|
|---|
| symbol
|
|---|
| term.selectChildTerms('is_a')
|
|---|
| getAssemblyStatistic(currentAssembly,'assemblyQuality').getValue().equals('Draft')
|
|---|
| term.comment != null
|
|---|
| property
|
|---|
| searchField
|
|---|
| plasmidStatsKeyList
|
|---|
| geneHistory!=null
|
|---|
| frameSegment.strand
|
|---|
| selectedHits != null
|
|---|
| components.distanceToGeneStartRenderBlock
|
|---|
| params.frameSegment.stop
|
|---|
| getRangeTranslator(true)
|
|---|
| currentGene.alleles.size() > 0 && visibleAlleles.size() == 0
|
|---|
| stop
|
|---|
| feature.start
|
|---|
| components.termHelpLoop.value.definition
|
|---|
| valueMap[label]
|
|---|
| '#'+mapName
|
|---|
| currentDrug
|
|---|
| summaryRowPairs
|
|---|
| page.getFunctionalCitations({'Gene Ontology'}).size() > 0
|
|---|
| hasHmmerHits
|
|---|
| showTextField
|
|---|
| 'release/argo/JnlpFile'
|
|---|
| previousGene neq null
|
|---|
| imageId
|
|---|
| currentLink.label
|
|---|
| (genomeStatsHeaderList+','+assemblyStatsHeadingList+','+plasmidStatsHeadingList)
|
|---|
| feature.name
|
|---|
| components.parentPath.index neq 0
|
|---|
| #{ 'form': components.editForm }
|
|---|
| feature.findXrefBySource('tbdbOperonPage') != null
|
|---|
| (locked&&statsExistForAssembly)
|
|---|
| canEditCurAnnotation()
|
|---|
| getStatistic(currentStatKey).statisticFeatures!=null&&getStatistic(currentStatKey).statisticFeatures.size()>0
|
|---|
| 'explain('+ explain +',\''+ theUrl +'\');'
|
|---|
| defaultFormat
|
|---|
| currentRow
|
|---|
| page.releasePage && page.allowResourceEditing && !page.isProductionServer
|
|---|
| gene
|
|---|
| context
|
|---|
| filename
|
|---|
| annotation neq null and listedAnnotation eq annotation ? 'active-annotation' : ''
|
|---|
| page.uncategorizedCitations(page.gene).size
|
|---|
| page.gene.transcripts neq null and page.gene.transcripts.size gt 0
|
|---|
| toolOptionsImage
|
|---|
| page.allowsLogin
|
|---|
| resources.displayTable.equals('Y')
|
|---|
| canEditGlossary
|
|---|
